chrom_wid <- 0.05
thinw <- 0.28
blstw <- 0.48
load("./EH23ideo.RData")
#
pEH23
load("./EH23ideo_ahplot.RData")
ahplot
ahplot + ggplot2::scale_color_brewer(palette="Paired")
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
ahplot + ggplot2::scale_color_brewer(palette="Paired", ggplot2::aes(alpha=0.04))
## Scale for colour is already present.
## Adding another scale for colour, which will replace the existing scale.
# scale_color_manual( values = my_pal )
tbl1 <- read.table("EH23a_EH23b_ortholog_blast_fractionation.txt", sep = " ")
tbl1[1:3, ]
## V1 V2 V3
## 1 EH23a.chr1.v1.g000010.t1 EH23b.chr1.v1.g000010.t1 chr1
## 2 EH23a.chr1.v1.g000020.t1 EH23b.chr1.v1.g000020.t1 chr1
## 3 EH23a.chr1.v1.g000030.t1 EH23b.chr1.v1.g000030.t1 chr1
all(sub("EH23a\\.", "", tbl1[, 1]) == sub("EH23b\\.", "", tbl1[, 2]))
## [1] FALSE
tbl2 <- read.table("quant.tsv", header = TRUE, sep = "\t")
tbl2[1:3, ]
## Sample Name Length EffectiveLength TPM
## 1 EH23_Early_Flower EH23a.chr1.v1.g000010.t1 3063 2849.169 2.464884
## 2 EH23_Early_Flower EH23a.chr1.v1.g000020.t1 768 554.402 0.000000
## 3 EH23_Early_Flower EH23a.chr1.v1.g000030.t1 1371 1157.169 1.367500
## NumReads
## 1 124.266
## 2 0.000
## 3 28.000
tbl2[1:3, ]
## Sample Name Length EffectiveLength TPM
## 1 EH23_Early_Flower EH23a.chr1.v1.g000010.t1 3063 2849.169 2.464884
## 2 EH23_Early_Flower EH23a.chr1.v1.g000020.t1 768 554.402 0.000000
## 3 EH23_Early_Flower EH23a.chr1.v1.g000030.t1 1371 1157.169 1.367500
## NumReads
## 1 124.266
## 2 0.000
## 3 28.000
table(tbl2$Sample)
##
## EH23_Early_Flower EH23_Foliage EH23_Foliage_12light
## 76968 76968 76968
## EH23_Late_Flower EH23_Roots EH23_Shoottips
## 76968 76968 76968
nrow(tbl2)
## [1] 461808
my_chroms <- sub("\\.v1.+", "", tbl2$Name)
table(my_chroms)
## my_chroms
## EH23a.chr1 EH23a.chr2 EH23a.chr3 EH23a.chr4 EH23a.chr5 EH23a.chr6 EH23a.chr7
## 30378 24630 24186 26208 22932 23406 18348
## EH23a.chr8 EH23a.chr9 EH23a.chrX EH23b.chr1 EH23b.chr2 EH23b.chr3 EH23b.chr4
## 23358 21780 31686 25410 21978 21606 23232
## EH23b.chr5 EH23b.chr6 EH23b.chr7 EH23b.chr8 EH23b.chr9 EH23b.chrX
## 18828 22116 16068 22182 18240 25236
tbl2$CHROM <- sub("EH23.\\.", "", my_chroms)
tbl2$hap <- sub("\\.chr.", "", my_chroms)
hist(log2(tbl2$TPM))
hist(log2(tbl2$TPM[ tbl2$hap == "EH23a"]))
hist(tbl2$TPM[ tbl2$hap == "EH23a"])
#hist(log2(tbl2$NumReads))
hist(log2(tbl2$NumReads[ tbl2$hap == "EH23a"]), breaks = seq(-10, 25, by = 1))
hist(log2(tbl2$NumReads[ tbl2$hap == "EH23b"]), breaks = seq(-10, 25, by = 1))
library(ggplot2)
tbl2[1:3, ]
## Sample Name Length EffectiveLength TPM
## 1 EH23_Early_Flower EH23a.chr1.v1.g000010.t1 3063 2849.169 2.464884
## 2 EH23_Early_Flower EH23a.chr1.v1.g000020.t1 768 554.402 0.000000
## 3 EH23_Early_Flower EH23a.chr1.v1.g000030.t1 1371 1157.169 1.367500
## NumReads CHROM hap
## 1 124.266 chr1 EH23a
## 2 0.000 chr1 EH23a
## 3 28.000 chr1 EH23a
p <- ggplot(tbl2, aes( x = log2(TPM) ))
p <- p + geom_histogram()
p <- p + theme_bw()
p <- p + scale_y_continuous(name = "Count (K)", breaks = seq(0, 60e3, by = 20e3), labels = seq(0, 60, by = 20))
p
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 201382 rows containing non-finite values (`stat_bin()`).
#library(scales)
#
#p + scale_y_continuous(labels = scientific)
ggpubr
library(ggpubr)
ggarrange(
plotlist = list(pEH23, ahplot),
labels = c("A", "B"),
label.x = 0,
label.y = c(1, 1.1),
ncol = 1, nrow = 2,
widths = 1, heights = c(2, 1)
)
library(ggpubr)
p1 <- ggarrange(
plotlist = list(pEH23, ahplot),
labels = c("A", "B"),
label.x = 0,
label.y = c(1, 1.1),
ncol = 1, nrow = 2,
widths = 1, heights = c(2, 1)
)
p2 <- ggarrange(
plotlist = list(p, p, p),
labels = c("C", "D", "E"),
label.x = 0,
label.y = c(1, 1.1),
ncol = 1, nrow = 3,
widths = 1, heights = c(2, 1, 1)
)
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 201382 rows containing non-finite values (`stat_bin()`).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 201382 rows containing non-finite values (`stat_bin()`).
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## Warning: Removed 201382 rows containing non-finite values (`stat_bin()`).
p3 <- ggarrange(
plotlist = list(p1, p2),
# labels = c("C", "D", "E"),
# label.x = 0,
# label.y = c(1, 1.1),
ncol = 2, nrow = 1,
widths = c(2, 1), heights = 1)
p3
ggsave( filename = "EH23_ideo_exp.tiff", device = "tiff",
width = 6.5,
height = 6.5,
#height = 9,
units = "in", dpi = 300,
compression = "lzw")